ImageJ -> Fiji updates related to LieberInstitute/visiumStitched#1

R/fetch_data.R

@@ -102,7 +102,7 @@ fetch_data <-
         "Visium_SPG_AD_Visium_wholegenome_modeling_results",
         "visiumStitched_brain_spe",
         "visiumStitched_brain_spaceranger",
-        "visiumStitched_brain_ImageJ_out"
+        "visiumStitched_brain_Fiji_out"
     ),
     destdir = tempdir(),
     eh = ExperimentHub::ExperimentHub(),
@@ -277,14 +277,14 @@ fetch_data <-
             file_name <- "visiumStitched_brain_spaceranger.zip"
             url <-
                 "https://www.dropbox.com/scl/fi/5jdoaukvhq3v7lk19228y/visiumStitched_brain_spaceranger.zip?rlkey=bdgjc6mgy1ierdad6h6v5g29c&dl=1"
-        } else if (type == "visiumStitched_brain_ImageJ_out") {
+        } else if (type == "visiumStitched_brain_Fiji_out") {
             tag <- "visiumStitched_brain_spatialLIBD"
             hub_title <- type
 
             ## While EH is not set-up
-            file_name <- "visiumStitched_brain_imagej_out.zip"
+            file_name <- "visiumStitched_brain_fiji_out.zip"
             url <-
-                "https://www.dropbox.com/scl/fi/bevo52e96f2kdwllf8dkk/visiumStitched_brain_imagej_out.zip?rlkey=ptwal8f5zxakzejwd0oqw0lhj&dl=1"
+                "https://www.dropbox.com/scl/fi/bevo52e96f2kdwllf8dkk/visiumStitched_brain_fiji_out.zip?rlkey=ptwal8f5zxakzejwd0oqw0lhj&dl=1"
         }
 
         file_path <- file.path(destdir, file_name)

inst/extdata/metadata_visiumStitched_brain.csv

@@ -1,4 +1,4 @@
 Title,Description,BiocVersion,Genome,SourceType,SourceUrl,SourceVersion,Species,TaxonomyId,Coordinate_1_based,DataProvider,Maintainer,RDataClass,DispatchClass,RDataPath,Tags
 visiumStitched_brain_spe,SpatialExperiment object at the spot-level for the spatially stitched human brain spatial transcriptomics data (n = 3) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.,3.19,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,June 11 2024,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres <[email protected]>,SpatialExperiment,Rds,spatialLIBD/spatialLIBD_files/visiumStitched_brain_spe.rds,visiumStitched_brain_spatialLIBD
 visiumStitched_brain_spaceranger,Spaceranger outputs for the spatially stitched human brain (spatial transcriptomics data (n = 3) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package. Can be used with visiumStitched::build_spe() to construct a SpatialExperiment.,3.19,GRCh38,Zip,https://bioconductor.org/packages/spatialLIBD,June 11 2024,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres <[email protected]>,list,Zip,spatialLIBD/spatialLIBD_files/visiumStitched_brain_spaceranger.zip,visiumStitched_brain_spatialLIBD
-visiumStitched_brain_ImageJ_out,Stitched PNG image and XML file from aligning human brain spatial transcriptomics data (n = 3) in ImageJ. Data to align was from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and is available through the spatialLIBD Bioconductor package.,3.19,GRCh38,Zip,https://bioconductor.org/packages/spatialLIBD,June 11 2024,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres <[email protected]>,list,Zip,spatialLIBD/spatialLIBD_files/visiumStitched_brain_imagej_out.zip,visiumStitched_brain_spatialLIBD
+visiumStitched_brain_Fiji_out,Stitched PNG image and XML file from aligning human brain spatial transcriptomics data (n = 3) in Fiji. Data to align was from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and is available through the spatialLIBD Bioconductor package.,3.19,GRCh38,Zip,https://bioconductor.org/packages/spatialLIBD,June 11 2024,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres <[email protected]>,list,Zip,spatialLIBD/spatialLIBD_files/visiumStitched_brain_imagej_out.zip,visiumStitched_brain_spatialLIBD

inst/scripts/make-metadata_visiumStitched_brain.R

@@ -6,11 +6,11 @@ outdir <- "spatialLIBD_files"
 pkgname <- "spatialLIBD"
 
 meta <- tibble(
-    Title = c("visiumStitched_brain_spe", "visiumStitched_brain_spaceranger", "visiumStitched_brain_ImageJ_out"),
+    Title = c("visiumStitched_brain_spe", "visiumStitched_brain_spaceranger", "visiumStitched_brain_Fiji_out"),
     Description = c(
         "SpatialExperiment object at the spot-level for the spatially stitched human brain spatial transcriptomics data (n = 3) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.",
         "Spaceranger outputs for the spatially stitched human brain (spatial transcriptomics data (n = 3) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package. Can be used with visiumStitched::build_spe() to construct a SpatialExperiment.",
-        "Stitched PNG image and XML file from aligning human brain spatial transcriptomics data (n = 3) in ImageJ. Data to align was from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and is available through the spatialLIBD Bioconductor package."
+        "Stitched PNG image and XML file from aligning human brain spatial transcriptomics data (n = 3) in Fiji. Data to align was from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and is available through the spatialLIBD Bioconductor package."
     ),
     BiocVersion = "3.19",
     Genome = "GRCh38",
@@ -29,7 +29,7 @@ meta <- tibble(
         outdir,
         c(
             "visiumStitched_brain_spe.rds", "visiumStitched_brain_spaceranger.zip",
-            "visiumStitched_brain_imagej_out.zip"
+            "visiumStitched_brain_fiji_out.zip"
         )
     ),
     Tags = "visiumStitched_brain_spatialLIBD"